[Rd] .Internal(quit(...)): system call failed: Cannot allocate memory

Jan Gorecki j@goreck| @end|ng |rom w|t@edu@p|
Tue Nov 24 15:48:54 CET 2020

As for other calls to system. I avoid calling system. In the past I
had some (to get memory stats from OS), but they were failing with
exactly the same issue. So yes, if I would add call to system before
calling quit, I believe it would fail with the same error.
At the same time I think (although I am not sure) that new allocations
made in R are working fine. So R seems to reserve some memory and can
continue to operate, while external call like system will fail. Maybe
it is like this by design, don't know.

Aside from this problem that is easy to report due to the warning
message, I think that gc() is choking at the same time. I tried to
make reproducible example for that, multiple times but couldn't, let
me try one more time.
It happens to manifest when there is 4e8+ unique characters/factors in
an R session. I am able to reproduce it using data.table and dplyr
(0.8.4 because 1.0.0+ fails even sooner), but using base R is not easy
because of the size. I described briefly problem in:

It would help if gcinfo() could take FALSE/TRUE/2L where 2L will print
even more information about gc, like how much time the each gc()
process took, how many objects it has to check on each level.

Best regards,

On Tue, Nov 24, 2020 at 1:05 PM Tomas Kalibera <tomas.kalibera using gmail.com> wrote:
> On 11/24/20 11:27 AM, Jan Gorecki wrote:
> > Thanks Bill for checking that.
> > It was my impression that warnings are raised from some internal
> > system calls made when quitting R. At that point I don't have much
> > control over checking the return status of those.
> > Your suggestion looks good to me.
> >
> > Tomas, do you think this could help? could this be implemented?
> I think this is a good suggestion. Deleting files on Unix was changed
> from system("rm") to doing that in C, and deleting the session directory
> should follow.
> It might also help diagnosing your problem, but I don't think it would
> solve it. If the diagnostics in R works fine and the OS was so
> hopelessly out of memory that it couldn't run any more external
> processes, then really this is not a problem of R, but of having
> exhausted the resources. And it would be a coincidence that just this
> particular call to "system" at the end of the session did not work.
> Anything else could break as well close to the end of the script. This
> seems the most likely explanation to me.
> Do you get this warning repeatedly, reproducibly at least in slightly
> different scripts at the very end, with this warning always from quit()?
> So that the "call" part of the warning message has .Internal(quit) like
> in the case you posted? Would adding another call to "system" before the
> call to "q()" work - with checking the return value? If it is always
> only the last call to "system" in "q()", then it is suspicious, perhaps
> an indication that some diagnostics in R is not correct. In that case, a
> reproducible example would be the key - so either if you could diagnose
> on your end what is the problem, or create a reproducible example that
> someone else can use to reproduce and debug.
> Best
> Tomas
> >
> > On Mon, Nov 23, 2020 at 7:10 PM Bill Dunlap <williamwdunlap using gmail.com> wrote:
> >> The call to system() probably is an internal call used to delete the session's tempdir().  This sort of failure means that a potentially large amount of disk space is not being recovered when R is done.  Perhaps R_CleanTempDir() could call R_unlink() instead of having a subprocess call 'rm -rf ...'.  Then it could also issue a specific warning if it was impossible to delete all of tempdir().  (That should be very rare.)
> >>
> >>> q("no")
> >> Breakpoint 1, R_system (command=command using entry=0x7fffffffa1e0 "rm -Rf /tmp/RtmppoKPXb") at sysutils.c:311
> >> 311     {
> >> (gdb) where
> >> #0  R_system (command=command using entry=0x7fffffffa1e0 "rm -Rf /tmp/RtmppoKPXb") at sysutils.c:311
> >> #1  0x00005555557c30ec in R_CleanTempDir () at sys-std.c:1178
> >> #2  0x00005555557c31d7 in Rstd_CleanUp (saveact=<optimized out>, status=0, runLast=<optimized out>) at sys-std.c:1243
> >> #3  0x00005555557c593d in R_CleanUp (saveact=saveact using entry=SA_NOSAVE, status=status using entry=0, runLast=<optimized out>) at system.c:87
> >> #4  0x00005555556cc85e in do_quit (call=<optimized out>, op=<optimized out>, args=0x555557813f90, rho=<optimized out>) at main.c:1393
> >>
> >> -Bill
> >>
> >> On Mon, Nov 23, 2020 at 3:15 AM Tomas Kalibera <tomas.kalibera using gmail.com> wrote:
> >>> On 11/21/20 6:51 PM, Jan Gorecki wrote:
> >>>> Dear R-developers,
> >>>>
> >>>> Some of the more fat scripts (50+ GB mem used by R) that I am running,
> >>>> when they finish they do quit with q("no", status=0)
> >>>> Quite often it happens that there is an extra stderr output produced
> >>>> at the very end which looks like this:
> >>>>
> >>>> Warning message:
> >>>> In .Internal(quit(save, status, runLast)) :
> >>>>     system call failed: Cannot allocate memory
> >>>>
> >>>> Is there any way to avoid this kind of warnings? I am using stderr
> >>>> output for detecting failures in scripts and this warning is a false
> >>>> positive of a failure.
> >>>>
> >>>> Maybe quit function could wait little bit longer trying to allocate
> >>>> before it raises this warning?
> >>> If you see this warning, some call to system() or system2() or similar,
> >>> which executes an external program, failed to even run a shell to run
> >>> that external program, because there was not enough memory. You should
> >>> be able to find out where it happens by checking the exit status of
> >>> system().
> >>>
> >>> Tomas
> >>>
> >>>
> >>>> Best regards,
> >>>> Jan Gorecki
> >>>>
> >>>> ______________________________________________
> >>>> R-devel using r-project.org mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>> ______________________________________________
> >>> R-devel using r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-devel

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